refactor(layout): 根目录脚本归位 src/ 与 scripts/，sql.d.ts 下沉到 db/

- bin.ts → src/bin.ts (生产入口归并到 src/，import 改用 #package + @/cli/*)
- compile.ts → scripts/compile.ts (开发期工具)
- embed-migrations.ts → scripts/embed-migrations.ts (codegen)
- src/sql.d.ts → src/server/db/sql.d.ts (与唯一消费者 migrations.gen.ts 共址)

效果：项目根从 3 个零散 .ts 减为 0 个，src/ 是完整应用源码，scripts/
明确区分开发期工具。所有 package.json scripts、AGENTS.md layout/CLI 章节、
compile.ts ENTRYPOINT 与 .js.map 清理路径同步更新。

验证：fix / typecheck / test 3/3 / build 570ms / compile 117M / docker
compose 全套（migrate 干净的 logger=cli.migrate JSON 日志、app /health
200、POST /api/todo/create 成功）。

scripts/embed-migrations.ts

@@ -0,0 +1,51 @@
+import { existsSync } from 'node:fs'
+import { readFile, writeFile } from 'node:fs/promises'
+import { z } from 'zod'
+
+const JOURNAL = './drizzle/meta/_journal.json'
+const OUTPUT = './src/server/db/migrations.gen.ts'
+
+const journalEntrySchema = z.object({
+  idx: z.number().int().nonnegative(),
+  tag: z.string().regex(/^\d{4}_[a-z0-9_]+$/),
+  when: z.number().int().nonnegative(),
+  breakpoints: z.boolean(),
+})
+const journalSchema = z.object({ entries: z.array(journalEntrySchema).default([]) })
+
+type JournalEntry = z.infer<typeof journalEntrySchema>
+
+const readJournalEntries = async (): Promise<JournalEntry[]> => {
+  if (!existsSync(JOURNAL)) {
+    return []
+  }
+  const raw: unknown = JSON.parse(await readFile(JOURNAL, 'utf-8'))
+  return journalSchema.parse(raw).entries.sort((a, b) => a.idx - b.idx)
+}
+
+const main = async () => {
+  const entries = await readJournalEntries()
+
+  const imports = entries
+    .map((e) => `import sql_${e.idx} from '#drizzle/${e.tag}.sql' with { type: 'text' }`)
+    .join('\n')
+
+  const arrayBody = entries.length
+    ? `[\n${entries.map((e) => `  { tag: '${e.tag}', sql: sql_${e.idx}, when: ${e.when}, breakpoints: ${e.breakpoints} },`).join('\n')}\n]`
+    : '[]'
+
+  const out = `// AUTO-GENERATED by \`bun run db:embed\`. Do not edit.
+${imports ? `${imports}\n` : ''}
+export type EmbeddedMigration = { tag: string; sql: string; when: number; breakpoints: boolean }
+
+export const embeddedMigrations: readonly EmbeddedMigration[] = ${arrayBody}
+`
+
+  await writeFile(OUTPUT, out)
+  console.log(`✓ ${OUTPUT} (${entries.length} migration${entries.length === 1 ? '' : 's'})`)
+}
+
+main().catch((err) => {
+  console.error('❌', err instanceof Error ? err.message : err)
+  process.exit(1)
+})